This analysis is to look at the MDS samples that were treated with the drug HTT homoharringtonine which is a translation inhibitor. There were only 2 samples for each treatment in this arm.
library(dplyr)
library(ggplot2)
library(DESeq2)
library(tximport)
library(readr)
library(tximportData)
library(readxl)
library(knitr)
library(tidyverse)
library(pheatmap)
library(RColorBrewer)
library(viridis)
library(ggrepel)
library(EnhancedVolcano)
library(fgsea)
library(limma)
library(VennDiagram)
library(UpSetR)
library(wesanderson)
library(kableExtra)
| Sample | patient | reads | %Q30 | Duplication rate | % reads with adapter | STAR alignment number | percent aligned | splices annotated | salmon mapping |
|---|---|---|---|---|---|---|---|---|---|
| CD123+ | HTB336 | 28161997 | 93 | 40 | 2.7 | 24795059 | 88.04 | 8802685 | 82.8170 |
| CD123+ | HTB61 | 17643949 | 90 | 29 | 2.5 | 13932164 | 78.96 | 3351481 | 68.1966 |
| CD123+ HHT | HTB336 | 17398408 | 93 | 42 | 2.7 | 15452341 | 88.81 | 5925372 | 87.9806 |
| CD123+ HHT | HTB61 | 22970807 | 93 | 33 | 2.6 | 20607839 | 89.71 | 4897461 | 75.8607 |
| SampleName | patient | cellType | percentrRNA |
|---|---|---|---|
| HTB61_CD123 | HTB61 | 123pos | 0.30 |
| HTB61_CD132_HHT | HTB61 | 123pos_HHT | 0.14 |
| HTB336_CD123_pos | HTB336 | 123pos | 0.38 |
| HTB336_CD123_pos_HHT | HTB336 | 123pos_HHT | 0.17 |
There are 5001 genes with more than 5 counts in all samples
We see a stronger correlation between patient than between sample type. One principle component is seperating on patient while the other is separating based on sample type.
| external_gene_name | padj | pvalue | log2FoldChange |
|---|---|---|---|
| FOS | 3.44e-16 | 2.40e-20 | -4.45 |
| LRPAP1 | 4.77e-14 | 6.65e-18 | -4.62 |
| TM4SF1 | 7.62e-11 | 1.59e-14 | 4.26 |
| OSM | 3.73e-10 | 1.30e-13 | -5.03 |
| HBA2 | 3.73e-10 | 1.26e-13 | -3.61 |
| ICAM1 | 2.69e-09 | 1.13e-12 | -2.96 |
| CD83 | 6.11e-09 | 2.98e-12 | -2.88 |
| HBA1 | 1.86e-07 | 1.04e-10 | -5.37 |
| WASH5P | 5.59e-07 | 3.51e-10 | -5.12 |
| ZNF14 | 5.77e-07 | 4.02e-10 | -2.74 |
| GSDME | 1.52e-06 | 1.16e-09 | -6.11 |
| RPS15 | 3.50e-06 | 3.17e-09 | -2.74 |
| ETV3 | 3.50e-06 | 3.18e-09 | -2.40 |
| SERTAD1 | 3.71e-06 | 3.62e-09 | -3.58 |
| ZNF133 | 5.18e-06 | 5.42e-09 | -5.74 |
| ZNF256 | 1.81e-05 | 2.02e-08 | -4.74 |
| IGLC2 | 1.98e-05 | 2.62e-08 | 6.19 |
| TRAF6 | 1.98e-05 | 2.39e-08 | -2.98 |
| GADD45B | 1.98e-05 | 2.51e-08 | -3.84 |
| ATP2A1 | 2.50e-05 | 3.48e-08 | 4.94 |
| RGS1 | 3.13e-05 | 4.58e-08 | -2.61 |
| SNHG17 | 4.09e-05 | 6.27e-08 | -2.44 |
| UCP2 | 4.69e-05 | 7.53e-08 | -2.56 |
| DPH6 | 5.47e-05 | 9.15e-08 | -3.96 |
| RASGEF1B | 6.50e-05 | 1.18e-07 | -2.09 |
| SIKE1 | 6.50e-05 | 1.14e-07 | -2.65 |
| SLC25A6 | 7.98e-05 | 1.56e-07 | -2.79 |
| ZNF625-ZNF20 | 7.98e-05 | 1.52e-07 | -3.09 |
| ANXA2 | 9.48e-05 | 1.92e-07 | 2.04 |
| CHMP1B-AS1 | 9.51e-05 | 1.99e-07 | -4.70 |
| NT5DC1 | 1.11e-04 | 2.40e-07 | -3.44 |
| PDE4B | 1.16e-04 | 2.68e-07 | -2.13 |
| BSG | 1.16e-04 | 2.67e-07 | -2.67 |
| PHYH | 1.20e-04 | 2.91e-07 | -3.23 |
| ZNF442 | 1.20e-04 | 2.93e-07 | -2.67 |
| CFAP20 | 1.60e-04 | 4.02e-07 | -2.53 |
| MCTP2 | 1.68e-04 | 4.53e-07 | -2.63 |
| C19orf48 | 1.68e-04 | 4.57e-07 | -2.40 |
| PUF60 | 1.68e-04 | 4.37e-07 | -2.85 |
| GSK3B | 1.71e-04 | 4.78e-07 | 3.60 |
| NUDT3 | 1.92e-04 | 5.50e-07 | 2.51 |
| NDUFS7 | 2.47e-04 | 7.24e-07 | -3.52 |
| PRMT9 | 2.69e-04 | 8.07e-07 | -3.32 |
| ATF3 | 2.87e-04 | 8.80e-07 | -2.68 |
| ESS2 | 3.10e-04 | 9.72e-07 | -4.32 |
| NUFIP1 | 3.21e-04 | 1.03e-06 | -4.80 |
| KLF10 | 4.05e-04 | 1.33e-06 | -2.21 |
| PLAUR | 5.10e-04 | 1.71e-06 | -2.09 |
| TNFAIP3 | 5.67e-04 | 1.94e-06 | -2.40 |
| IGHM | 5.75e-04 | 2.05e-06 | -2.91 |
| MUC12 | 5.75e-04 | 2.03e-06 | -5.51 |
| NLRP3 | 6.16e-04 | 2.27e-06 | -2.49 |
| IL1RL1 | 6.16e-04 | 2.28e-06 | -3.85 |
| ABHD10 | 6.52e-04 | 2.46e-06 | -3.98 |
| ZNF140 | 6.59e-04 | 2.53e-06 | -2.21 |
| ARL4A | 6.79e-04 | 2.70e-06 | -1.94 |
| CXCR2 | 6.79e-04 | 2.67e-06 | -9.28 |
| NLE1 | 6.99e-04 | 2.83e-06 | -4.05 |
| NCKAP1 | 1.05e-03 | 4.34e-06 | 3.59 |
| PPP1R15A | 1.08e-03 | 4.51e-06 | -2.76 |
| LTBP1 | 1.13e-03 | 4.80e-06 | -7.56 |
| NANS | 1.14e-03 | 4.92e-06 | -2.19 |
| WDR43 | 1.26e-03 | 5.53e-06 | -1.99 |
| CDKN1A | 1.27e-03 | 5.68e-06 | -2.04 |
| NFU1 | 1.27e-03 | 5.76e-06 | -3.16 |
| CIDEB | 1.27e-03 | 5.90e-06 | 6.16 |
| RPL8 | 1.27e-03 | 5.94e-06 | -1.77 |
| HAUS7 | 1.30e-03 | 6.24e-06 | -3.36 |
| HEMK1 | 1.30e-03 | 6.26e-06 | -2.35 |
| FFAR3 | 1.45e-03 | 7.18e-06 | -8.78 |
| ZNF394 | 1.45e-03 | 7.10e-06 | -2.08 |
| BTBD8 | 1.53e-03 | 7.70e-06 | -8.97 |
| MTX2 | 1.54e-03 | 7.83e-06 | -4.46 |
| GRAP | 1.55e-03 | 7.98e-06 | -9.19 |
| IFFO1 | 1.72e-03 | 8.98e-06 | -8.07 |
| TNFAIP6 | 1.72e-03 | 9.11e-06 | -2.49 |
| PLA2G12A | 1.75e-03 | 9.41e-06 | -3.71 |
| CLEC4E | 1.80e-03 | 9.80e-06 | -5.24 |
| RNF138 | 1.85e-03 | 1.02e-05 | -2.14 |
| PTRHD1 | 1.85e-03 | 1.03e-05 | -3.55 |
| HNRNPDL | 1.87e-03 | 1.06e-05 | -1.87 |
| RALY | 1.92e-03 | 1.10e-05 | 3.82 |
| IVD | 1.95e-03 | 1.13e-05 | -2.50 |
| R3HCC1 | 2.18e-03 | 1.28e-05 | -3.98 |
| PMAIP1 | 2.91e-03 | 1.73e-05 | -2.40 |
| H1-4 | 2.91e-03 | 1.75e-05 | -3.24 |
| FOSB | 3.00e-03 | 1.82e-05 | -2.03 |
| WDFY2 | 3.06e-03 | 1.90e-05 | 2.33 |
| ARID4A | 3.06e-03 | 1.88e-05 | -1.90 |
| NKTR | 3.07e-03 | 1.93e-05 | -1.91 |
| EIF1 | 3.46e-03 | 2.19e-05 | -1.97 |
| ASH2L | 3.59e-03 | 2.30e-05 | -2.17 |
| USP3 | 3.71e-03 | 2.41e-05 | -2.25 |
| SNX17 | 4.02e-03 | 2.64e-05 | -2.79 |
| CYB5R4 | 4.22e-03 | 2.80e-05 | -2.17 |
| POLR2E | 4.28e-03 | 2.89e-05 | -3.21 |
| BTG2 | 4.28e-03 | 2.89e-05 | -2.40 |
| RNF144B | 4.38e-03 | 3.02e-05 | -2.40 |
| LMAN2 | 4.38e-03 | 3.00e-05 | -2.78 |
| CXCR5 | 4.38e-03 | 3.08e-05 | -9.00 |
| IRAK2 | 4.38e-03 | 3.08e-05 | -2.81 |
| H2AC19 | 4.41e-03 | 3.14e-05 | -5.21 |
| USP11 | 4.52e-03 | 3.25e-05 | -2.49 |
| GFI1B | 4.53e-03 | 3.32e-05 | -2.86 |
| ACSF3 | 4.53e-03 | 3.30e-05 | -3.43 |
| DOCK7 | 4.54e-03 | 3.40e-05 | 3.45 |
| SLC7A6OS | 4.54e-03 | 3.36e-05 | -3.84 |
| HSPA5 | 4.54e-03 | 3.42e-05 | -1.82 |
| JDP2 | 5.26e-03 | 4.00e-05 | 4.12 |
| 5.35e-03 | 4.10e-05 | -8.86 | |
| ZBTB48 | 5.53e-03 | 4.28e-05 | -2.76 |
| RGS2 | 6.13e-03 | 4.83e-05 | -2.06 |
| 6.13e-03 | 4.82e-05 | 4.33 | |
| ZNF136 | 6.19e-03 | 4.92e-05 | -1.96 |
| SAMSN1 | 6.33e-03 | 5.12e-05 | -1.74 |
| ZFP36 | 6.33e-03 | 5.16e-05 | -2.29 |
| SPPL2A | 6.33e-03 | 5.09e-05 | 2.38 |
| SRSF10 | 6.50e-03 | 5.34e-05 | -1.67 |
| POC5 | 6.79e-03 | 5.68e-05 | -3.00 |
| SNAPC1 | 6.79e-03 | 5.68e-05 | -2.08 |
| HLA-E | 7.10e-03 | 5.99e-05 | -1.62 |
| CDC37L1 | 7.17e-03 | 6.10e-05 | -2.62 |
| SDE2 | 7.40e-03 | 6.35e-05 | -1.76 |
| MBNL3 | 7.42e-03 | 6.42e-05 | -4.55 |
| DNAJB1 | 8.24e-03 | 7.18e-05 | -1.82 |
| FLRT2 | 8.45e-03 | 7.42e-05 | 3.48 |
| MIR222HG | 8.68e-03 | 7.72e-05 | 2.52 |
| CISH | 8.68e-03 | 7.75e-05 | -3.55 |
| HIF1AN | 9.24e-03 | 8.31e-05 | -2.14 |
| UGGT2 | 9.36e-03 | 8.49e-05 | -4.59 |
| DDA1 | 9.43e-03 | 8.61e-05 | -3.39 |
| LIPN | 1.00e-02 | 9.20e-05 | -8.60 |
###MA plots
##Displaying a table of ordered pathways
#plot the waterfall results
##repeating with KEGG pathways
I can do this for any of interest, just let me know
I can do this for any of interest, just let me know